Permanent Exhibition
The permanent exhibition placed over several levels is divided into 2 main parts. The first is devoted to Byzantium (4th -15th Century A.D.) and contains 1,200 artifacts and the second entitled from Byzantium to the modern era presents 1,500 artworks dating from the 15th to 20th Century. The permanent collection is housed in an underground multi-level building created by Manos Perrakis, which is situated underneath the complex of Villa Illisia.

Icons & Wood carvings
The impressive Byzantine and Post-Byzantine collection of 3,000 icons covers the long chronological spectrum and comes from all over Greece, Asia Minor, the Balkans, and Russia. Wood carvings and episcopal thrones complete the collection.

Wall paintings
Wall-painting fragments are presented, dating from the 5th & 6th to the 18th Century A.D.

Textiles
The Collection includes about 1,000 textiles, mainly ecclesiastical artifacts, priestly vestments and liturgical cloths from all over Greece, the Balkans and Asia Minor which date from the 5th Century to the 20th.

Sculpture
The sculpture collection includes some 2,000 architectural and decorative pieces, mostly made of marble that range from the early Christian era to the late 18th Century and come from Christian monuments in Athens, the rest of Greece, and Asia Minor.

Paintings
The Collection includes 110 religious paintings, icons, and depictions of the pilgrimage shrines of the Holy Land.

Manuscripts, Codices, Early Printed Books
The Collection includes 500 Byzantine and post-Byzantine manuscripts, dating from the 6th to the 19th Century, 300 early printed books from the 16th and the 19th Century and 600 woodcuts, etchings and lithographs, dated from the 18th and 19th Century. Of particular importance is also the museum’s collection of drawings, which includes more than 3,200 works on paper.
 

Mosaics
The Collection includes more than 50 pieces of mosaic floor that were found during excavations in an Early Christian basilica that stood close to Illisos River and in 2 sites in Euripidou and in Dioysiou Areopagitou Street in Athens. The parts of the mosaic pavement from the Dionysiou Areopagitou excavation were covering the floor entrance of the Museum from 1970 until 2014

Minor Art
The Collection contains about 6,000 objects, mainly ecclesiastical artefacts, about 1,000 coins issued by the emperors of Constantinople from the 4th to the 14th Century, clay lamps and seals, small flasks for holy oil, lead seals of imperial and church officials, carved wooden crosses with metal revetment, and a number of brass pectoral cross-reliquaries.

I & D Passas Foundation Collection
Since 2005, the largest part of the Passas Foundation is hosted in the museum as a 20-year loan. The Passas Foundation Collection includes 580 statuettes and vases made of ivory and clay, porcelain vases and marble sculptures, coming mainly from China, Japan, and India. 173 copies of Western European paintings, dated from the late 19th Century to the beginning of the 20th Century, and 90 porcelain works from Western Europe, dating from the late 19th to the first half of the 20th Century.